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Crystal Structure of PKD2 Phosphopeptide Bound to Human Class I MHC HLA-A2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 17% PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.65 53.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.8 α = 90 b = 54.8 β = 105 c = 75.8 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD SATURN 2007-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5417
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.6 20 96 0.033 29.95 6.4 59358 -3 26.066
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.7 81.7 0.441 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.6 19.63 59357 3001 96.18 0.203 0.202 0.1997 0.232 0.2289 RANDOM 19.446
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.848 r_dihedral_angle_4_deg 19.891 r_dihedral_angle_3_deg 11.898 r_dihedral_angle_1_deg 5.755 r_scangle_it 3.286 r_scbond_it 2.224 r_mcangle_it 1.386 r_angle_refined_deg 1.308 r_mcbond_it 0.916 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.848 r_dihedral_angle_4_deg 19.891 r_dihedral_angle_3_deg 11.898 r_dihedral_angle_1_deg 5.755 r_scangle_it 3.286 r_scbond_it 2.224 r_mcangle_it 1.386 r_angle_refined_deg 1.308 r_mcbond_it 0.916 r_nbtor_refined 0.294 r_nbd_refined 0.188 r_xyhbond_nbd_refined 0.127 r_symmetry_hbond_refined 0.124 r_symmetry_vdw_refined 0.121 r_chiral_restr 0.1 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3157 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 16
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing